Sesame is a historic oilseed crop cultivated globally. The crop harbors natural antioxidants in plant tissues, including leaves, stems, and seeds. Understanding flower development mechanisms is crucial for higher yield and quality. However, the physiological and molecular aspects of threeand single-capsule flower development in sesame remain unexplored. This study investigated the transcriptome during sesame flower development, focusing on three-capsule (Arslanbey) and singlecapsule (Hatipoğlu) cultivars during 2017-2018. Physiological analyses (iron chelation, DPPH, FRAP) and qRT-PCR of APETALA1, APETALA2, SPL4, SOC1, AT4G37770, SILPT3, and beta-glucosidase genes were conducted. Metal-iron chelation, FRAP, and DPPH in leaf tissues indicated higher values in the single-capsule cultivar, while catalase and peroxidase activity were higher in the three-capsule cultivar. Expression analyses at different weeks post-flowering showed peak levels for AP1, AP2, SPL4, SILPT3, and beta-glucosidase at 8W-H (8th-Hatipoğlu) in the single-capsule cultivar, and for SOC1 and AT4G37770 at 9W-H (9th-Hatipoğlu). Capsule-related gene expression over 9 weeks revealed 8W-H (8^th-Hatipoğlu). As abundant for APETALA1, APETALA2, SPL4, SILPT3, and beta-glucosidase, while 9W-H (9^th-Hatipoğlu) was abundant for SOC1 and AT4G37770. In this study, which was carried out to examine the factors affecting the encapsulation status of single-capsule and three-capsule sesame varieties, evaluations were made based on the data obtained as a result of the observations and analysis. All analyses have shown that the single and triple encapsulation phenomena are quite complex and depend on multiple gene mechanisms and multiple biochemicals. In summary, our study unveils the intricate genetic and biochemical factors influencing capsule development in single-capsule and three-capsule sesame varieties. These findings offer valuable insights for future breeding strategies and molecular studies in sesame and related crops.